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At least 181 records · Page 10

Deeply conserved synteny and the evolution of metazoan chromosomes

Animal genomes show networks of deeply conserved gene linkages whose phylogenetic scope and chromosomal context remain unclear. Here, we report chromosome-scale conservation of synteny among bilaterians, cnidarians, and sponges and use comparative analysis to reconstruct ancestral chromosomes across major animal groups. Comparisons among diverse metazoans reveal the processes of chromosome evolution that produced contemporary karyotypes from their Precambrian progenitors. On the basis of these findings, we introduce a simple algebraic representation of chromosomal change and use it to establish a unified systematic framework for metazoan chromosome evolution. We find that fusion-with-mixing, a previously unappreciated mode of chromosome change, has played a central role. We find that relicts of several metazoan chromosomal units are preserved in unicellular eukaryotes. These conserved pre-metazoan linkages include the chromosomal unit that encodes the most diverse set of metazoan homeobox genes, suggesting a candidate genomic context for the early diversification of this key gene family.

59 BASIC BIOLOGICAL SCIENCES↗

Conserved conformational dynamics determine enzyme activity

Homologous enzymes often exhibit different catalytic rates despite a fully conserved active site. The canonical view is that an enzyme sequence defines its structure and function and, more recently, that intrinsic protein dynamics at different time scales enable and/or promote catalytic activity. Here, we show that, using the protein tyrosine phosphatase PTP1B, residues surrounding the PTP1B active site promote dynamically coordinated chemistry necessary for PTP1B function. However, residues distant to the active site also undergo distinct intermediate time scale dynamics and these dynamics are correlated with its catalytic activity and thus allow for different catalytic rates in this enzyme family. We identify these previously undetected motions using coevolutionary coupling analysis and nuclear magnetic resonance spectroscopy. Our findings strongly indicate that conserved dynamics drives the enzymatic activity of the PTP family. Characterization of these conserved dynamics allows for the identification of novel regulatory elements (therapeutic binding pockets) that can be leveraged for the control of enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

Gaussian null coordinates, near-horizon geometry and conserved charges on the horizon of extremal nondilatonic black p-branes

In this paper, we examine the emergence of conserved charges on the horizon of a particular class of extremal nondilatonic black [Formula: see text]-branes (which reduce to extremal dilatonic black holes in [Formula: see text] dimensions upon toroidal compactification) in the presence of a probe massless scalar field in the bulk. This result is achieved by writing the black [Formula: see text]-brane geometry in a Gaussian null coordinate system which allows us to get a nonsingular near-horizon geometry description. We find that the near-horizon geometry is [Formula: see text] and that the [Formula: see text] section has an internal structure which can be seen as a warped product of [Formula: see text] in Gaussian null coordinates. We show that the bulk scalar field satisfying the field equations is expanded in terms of nonnormalizable and normalizable modes, which for certain suitable quantization conditions are well-behaved at the boundary of [Formula: see text] space. Furthermore, we show that picking the normalizable modes results in the existence of conserved quantities on the horizon. We discuss the impact of these conserved quantities in the late-time regime.

Astronomy & Astrophysics↗

AmeriFlux FLUXNET-1F US-xSC NEON Smithsonian Conservation Biology Institute (SCBI)

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-xSC NEON Smithsonian Conservation Biology Institute (SCBI). This is the FLUXNET version of the carbon flux data for the site US-xSC NEON Smithsonian Conservation Biology Institute (SCBI) produced by applying the standard ONEFlux (1F) software. Site Description - The Smithsonian Conservation Biology Institute (SCBI) site is a mid-continent forested eastern deciduous site, species include Oaks, Hickories, and Ash, and contains well defined ground cover and understory strata.

Network), NEON (National Ecological Observatory↗

Assessing Nutrient and Carbon Responses to Agricultural Conservation Practices in Two Midwest Watersheds

The United States is undertaking efforts to transition to a low-carbon economy in response to the heightened impacts of climate change, which are largely attributed to decades of carbon-intensive development. A concerted effort by the energy sector to achieve net-zero carbon emissions is aimed at strategically reducing the carbon footprint of the energy supply chain, particularly in the production of feedstocks for biofuels. The production of biofuels relies heavily on land use and management practices in biomass cultivation. Among other factors, soil organic carbon (SOC) plays a crucial role in the biofuel carbon cycle, impacting land productivity, greenhouse gas emissions, and water quality. The process of carbon drawdown during plant growth and storage helps to mitigate the release of carbon dioxide (CO 2 ) into the atmosphere. Another key parameter is the release of nitrous oxide (N 2 O) — a potent greenhouse gas with a global warming potential 273 times that of CO 2 — from soil. While prioritizing low-carbon production, sustainable bioenergy also necessitates improved water quality and ecosystem services. Agricultural conservation practices can contribute to enhanced soil health and reduce nutrient and sediment loss into streams. However, studies that explore the broader impact of these practices on soil carbon storage and N 2 O emissions at a watershed scale are limited. Specifically, our understanding of how low-carbon feedstock production and management affect nutrient cycle dynamics is incomplete. This study assesses watershed responses to land management practices in two agriculturally dominant watersheds: the Raccoon River watershed and the Southfork of Iowa River watershed. The study focuses on carbon and nutrient dynamics, characterizing spatial and temporal variations in SOC, N 2 O, and nutrient loadings to examine the relationship between nutrient and carbon responses and agricultural conservation practices. The study employs the newly developed Soil Water Analysis Tool for Carbon (SWAT-C) model, calibrated using 20 years’ of climate and water monitoring data, to simulate and evaluate two agricultural conservation practices: no-till and crop residue harvest with cover crop planting. We compared the calibrated SWAT-C model with a historical baseline model, which allowed us to analyze various aspects of the watershed, including stream flow, suspended sediments, nitrogen, phosphorus, organic carbon, SOC at different depths, and N 2 O emissions from topsoil. Our SWAT-C modeling results indicate that, compared with results from the historical baseline model, no-till practices are positively correlated with SOC accumulation, reduced N 2 O emissions, and decreased soil loss. We also observed no change or slightly increased nitrogen and phosphorus loss to water bodies in the watersheds compared with the baseline. Conversely, crop residue harvest with cover crop planting improved water quality by reducing nutrient and soil losses but also increased N 2 O emissions. This SWAT-C modeling study establishes the groundwork for further smaller-scale and/or sub-basin-level assessments of nitrogen, phosphorus, and carbon cycles. It provides valuable science-based insights to inform policy decisions — particularly in the context of transitioning to biofuel feedstock production in these watersheds — by addressing concerns about nutrient exports to local water bodies and, ultimately, the Mississippi River.

54 ENVIRONMENTAL SCIENCES↗

Sister Rod Destructive Examinations (FY23) Appendix F3: Uncertainty and Conservative Bias in the Cyclic Integrated Reversible-Bending Fatigue Test

The development and application of the Cyclic Integrated Reversible-Bending Fatigue Tester (CIRFT) has been documented over the past 10 years. The CIRFT system was developed in collaboration with the U.S. Nuclear Regulatory Commission (NRC) to address the concern that high-burnup fuel rod fatigue performance was degraded compared to cladding-only behavior. Fatigue data measured by CIRFT on high-burnup fuel rods were then used by the NRC to develop a fatigue response curve for pressurized water reactor fuel rods with Zircaloy-4 cladding in NUREG-2224. Subsequently, CIRFT has been used in the sister rod project to test whether reoriented hydrides associated with vacuum drying influenced the fatigue lifetime, to extend the fatigue testing database to include fuel rods with ZIRLO cladding, and to add to the experience on both Zircaloy-4 and M5 cladding. These data will be used as a reference for subsequent characterization of fuel rods removed from the high-burnup demonstration cask to better understand the effects of long-term dry storage, which can be thought of as a multiyear elevated temperature anneal. The objective of fatigue testing is to provide data that can be used to develop a best-estimate fatigue curve and a conservative fatigue design curve that accounts for uncertainty and can be compared with actual transportation conditions. The process for defining a design fatigue curve for commercial used fuel rods was developed by Oak Ridge National Laboratory (ORNL) in FY22. One issue noted in the fatigue evaluation was that the calculated combined uncertainty in the strain amplitude values determined from the measured data was large. It was proposed then to directly measure the uncertainty in the strain amplitude to either validate the calculated combined uncertainty or update the uncertainty based on the measurement data. Thus, the purpose of this appendix is to document the measured uncertainty in the strain amplitude data. In the process, it was determined that there has been a conservative bias in the calculated strain amplitude that is small enough to be within the measurement uncertainty. This observation is discussed herein, and a case is made to continue to include the conservative bias in the data.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Digital Tools for the Preventive Conservation of Built Heritage: The Church of Santa Ana in Seville

Historic Building Information Modelling (HBIM) plays a pivotal role in heritage conservation endeavours, offering a robust framework for digitally documenting existing structures and supporting conservation practices. However, HBIM’s efficacy hinges upon the implementation of case-specific approaches to address the requirements and resources of each individual asset and context. This paper defines a flexible and generalisable workflow that encompasses various aspects (i.e., documentation, surveying, vulnerability assessment) to support risk-informed decision making in heritage management tailored to the peculiar conservation needs of the structure. This methodology includes an initial investigation covering historical data collection, metric and condition surveys and non-destructive testing. The second stage includes Finite Element Method (FEM) modelling and structural analysis. All data generated and processed are managed in a multi-purpose HBIM model. The methodology is tested on a relevant case study, namely, the church of Santa Ana in Seville, chosen for its historical significance, intricacy and susceptibility to seismic action. The defined level of detail of the HBIM model is sufficient to inform the structural analysis, being balanced by a more accurate representation of the alterations, through linked orthophotos and a comprehensive list of alphanumerical parameters. This ensures an adequate level of information, optimising the trade-off between model complexity, investigation time requirements, computational burden and reliability in the decision-making process. Field testing and FEM analysis provide valuable insight into the main sources of vulnerability in the building, including the connection between the tower and nave and the slenderness of the columns.

Chaves, Estefanía↗

Evolutionary Diversification of Host-Targeted Bartonella Effectors Proteins Derived from a Conserved FicTA Toxin-Antitoxin Module

Proteins containing a FIC domain catalyze AMPylation and other post-translational modifications (PTMs). In bacteria, they are typically part of FicTA toxin-antitoxin modules that control conserved biochemical processes such as topoisomerase activity, but they have also repeatedly diversified into host-targeted virulence factors. Among these, Bartonella effector proteins (Beps) comprise a particularly diverse ensemble of FIC domains that subvert various host cellular functions. However, no comprehensive comparative analysis has been performed to infer molecular mechanisms underlying the biochemical and functional diversification of FIC domains in the vast Bep family. Here, we used X-ray crystallography, structural modelling, and phylogenetic analyses to unravel the expansion and diversification of Bep repertoires that evolved in parallel in three Bartonella lineages from a single ancestral FicTA toxin-antitoxin module. Our analysis is based on 99 non-redundant Bep sequences and nine crystal structures. Inferred from the conservation of the FIC signature motif that comprises the catalytic histidine and residues involved in substrate binding, about half of them represent AMP transferases. A quarter of Beps show a glutamate in a strategic position in the putative substrate binding pocket that would interfere with triphosphate-nucleotide binding but may allow binding of an AMPylated target for deAMPylation or another substrate to catalyze a distinct PTM. The β-hairpin flap that registers the modifiable target segment to the active site exhibits remarkable structural variability. The corresponding sequences form few well-defined groups that may recognize distinct target proteins. The binding of Beps to promiscuous FicA antitoxins is well conserved, indicating a role of the antitoxin to inhibit enzymatic activity or to serve as a chaperone for the FIC domain before translocation of the Bep into host cells. Taken together, our analysis indicates a remarkable functional plasticity of Beps that is mostly brought about by structural changes in the substrate pocket and the target dock. These findings may guide future structure–function analyses of the highly versatile FIC domains.

59 BASIC BIOLOGICAL SCIENCES↗

Planning and programing in the soil conservation service

The historical base is presented for the framework plan for soil conservation. Conservation effects, resource management systems, and accomplishments, activities, and costs of the Soil Conservation Service are discussed.

Gray, R. M.↗

Conservation of wave action

It is pointed out that two basic principles appear in the theory of wave propagation, including the existence of a phase variable and a law governing the intensity, in terms of a conservation law. The concepts underlying such a conservation law are explored. The waves treated are conservative in the sense that they obey equations derivable from a variational principle applied to a Lagrangian functional. A discrete oscillating system is considered. The approach employed also permits in a natural way the definition of a local action density and flux in problems in which the waves are modal or general.

Hayes, W. D.↗

An assessment of the benefits of the use of NASA developed fuel conservative technology in the US commercial aircraft fleet

Cost and benefits of a fuel conservative aircraft technology program proposed by NASA are estimated. NASA defined six separate technology elements for the proposed program: (a) engine component improvement (b) composite structures (c) turboprops (d) laminar flow control (e) fuel conservative engine and (f) fuel conservative transport. There were two levels postulated: The baseline program was estimated to cost $490 million over 10 years with peak funding in 1980. The level two program was estimated to cost an additional $180 million also over 10 years. Discussions with NASA and with representatives of the major commercial airframe manufacturers were held to estimate the combinations of the technology elements most likely to be implemented, the potential fuel savings from each combination, and reasonable dates for incorporation of these new aircraft into the fleet.

Source record↗

Electric load management and energy conservation

Electric load management and energy conservation relate heavily to the major problems facing power industry at present. The three basic modes of energy conservation are identified as demand reduction, increased efficiency and substitution for scarce fuels. Direct and indirect load management objectives are to reduce peak loads and have future growth in electricity requirements in such a manner to cause more of it to fall off the system's peak. In this paper, an overview of proposed and implemented load management options is presented. Research opportunities exist for the evaluation of socio-economic impacts of energy conservation and load management schemes specially on the electric power industry itself.

Kheir, N. A.↗

The artificial compression method for computation of shocks and contact discontinuities. I - Single conservation laws

The paper discusses the use of the artificial compression method for the computation of discontinuous solutions of a single conservation law by finite difference methods. The single conservation law has either a shock or a contact discontinuity. Any monotone finite difference scheme applied to the original equation smears the discontinuity, while the same scheme applied to the equation modified by an artificial compression flux produces steady progressing profiles. If L is any finite difference scheme in conservation form and C is an artificial compressor, the split flux artificial compression method CL is a corrective scheme: L smears the discontinuity while propagating it; C compresses the smeared transition toward a sharp discontinuity. Numerical implementation of artificial compression is described.

Harten, A.↗

Coefficient matrices for implicit finite difference solution of the inviscid fluid conservation law equations

Although the Navier-Stokes equations describe most flows of interest in aerodynamics, the inviscid conservation law equations may be used for small regions with viscous forces. Thus, Euler equations and several time-accurate finite difference procedures, explicit and implicit, are discussed. Although implicit techniques require more computational work, they permit larger time steps to be taken without instability. It is noted that the Jacobian matrices for Euler equations in conservation-law form have certain eigenvalue-eigenvector properties which may be used to construct conservative-form coefficient matrices. This reduces the computation time of several implicit and semiimplicit schemes. Extensions of the basic approach to other areas are suggested.

Steger, J. L.↗

Simulation study of the effect of fuel-conservative approaches on ATC procedures and terminal area capacity

Fuel-conservative procedures have been investigated using real-time air traffic control simulations linked to two piloted simulators. The fuel-conservative procedures studied were profile descents and two types of landing approaches. The investigation determined the effect of these procedures on the ATC system and terminal area capacity. It examined the mixing of aircraft executing fuel-conservative approaches with those executing conventional approaches. The results indicate a systems fuel savings for the landing approaches under all tested conditions except at, or near, maximum system capacity. Also, there is a fuel savings and reduced controller workload for the profile descent procedures.

Tobias, L.↗

Energy conserving norms for the solution of hyperbolic systems of partial differential equations

The hyperbolic system of partial differential equations with a real constant square coefficient matrix A is considered. The problem of finding an energy conserving norm for the solution of the system is reduced to the problem of characterizing those matrices appearing in the boundary conditions which satisfy two specific matrix equations. Necessary and sufficient conditions on the coefficient matrix A and the matrices appearing in boundary conditions are derived for an energy conserving norm. The conditions serve as criteria on a given system which determine whether or not the solution will have its energy conserved in some norm. Examples of specific systems and boundary conditions are also provided.

Gunzburger, M. D.↗

Simulation study of the operational effects of fuel-conservative approaches

Fuel-conservative procedures have been investigated using real-time air traffic control simulations linked to two piloted simulators. The fuel-conservative procedures studied were profile descents and two types of landing approaches, delayed flap and IATA. The investigation determined the effect of these procedures on the ATC system operation. It examined the mixing of aircraft executing fuel-conservative approaches with those executing conventional approaches. The most difficult approach type mix of traffic was found to be 50% conventional and 50% delayed flap. However, for the test scenario chosen, arrival rates of at least 30 aircraft per hour were feasible and resulted in a net average fuel saving, even for the most difficult mix. Also, there is a fuel savings and reduced controller workload for the profile descent procedures.

Tobias, L.↗

Conservative full-potential calculations for axisymmetric, transonic flow

A conservative, finite-difference, full-potential relaxation code has been developed to solve transonic flow around axisymmetric or nonlifting, planar, two-dimensional bodies. The program utilizes the artificial compressibility method to provide an upwind bias in supersonic regions. Calculated examples include a wide variety of axisymmetric and planar two-dimensional shapes with various blunt, pointed and open ends in subsonic, transonic, and low supersonic free streams. Comparisons between conservative and nonconservative full-potential calculations show perfect agreement at convergence when the flow is entirely subsonic. Noticeable differences exist, however, between the conservative and nonconservative solutions for transonic flows with shocks.

Green, L. L.↗